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The salt marsh harvest mouse (Reithrodontomys raviventris; RERA) is an endangered species endemic to the coastal wetlands of the San Francisco Estuary, California. RERA are specialized to saline coastal wetlands, and their historical range has been severely impacted by landscape conversion and the introduction of non-native plant and rodent species. A better understanding of their diet is needed to assess habitat quality, particularly in relation to potential competitors. We investigated three questions using DNA metabarcoding with ITS2 and trnL markers: (1) Do RERA specialize on the native plant, pickleweed (Salicornia pacifica), (2) Do RERA consume non-native plants, and (3) What is the dietary niche breadth and overlap with three sympatric native and non-native rodents? RERA diet was dominated by two plants, native Salicornia and non-native salt bush (Atriplex spp.), but included 48 plant genera. RERA diet breadth was narrowest in fall, when they consumed the highest frequencies of Salicornia and Atriplex, and broadest in spring, when the frequencies of these two plants were lowest. Diet breadth was slightly lower for RERA than for co-occurring species in pairwise comparisons. All four species consumed similarly high frequencies of wetland plants, but RERA consumed fewer grasses and upland plants, suggesting that it may be less suited to fragmented habitat than sympatric rodents. Diet overlap was lowest between RERA and the native California vole (Microtis californicus). In contrast, RERA diet overlapped substantially with the native western harvest mouse (R. megalotis) and non-native house mouse (Mus musculus), suggesting potential for competition if these species become sufficiently abundant.

We used mitochondrial sequences and nuclear microsatellites to investigate population structure of gray foxes (Urocyon cinereoargenteus) and the evolutionary origins of the endemic island fox (Urocyon littoralis), which first appeared in the northern Channel Islands

[Abstracts are not presented for essays. -The SFEWS Editors.]

The salt marsh harvest mouse (SMHM, Reithrodontomys raviventris) is an endangered species, endemic to the San Francisco Estuary. Despite being protected for almost half a century and being included in a large number of recovery, restoration, and management plans, significant data gaps hinder conservation and management of the species, a challenge further complicated by developing threats such as climate change. In this review, we present the current state of knowledge; highlight research gaps on habitat requirements and distribution, taxonomic status and genetic structure, physiology, reproduction and demographics, population dynamics, and behavior and community interactions; and present an overview of threats to the species. Our review indicates that substantial data gaps exist; although some aspects of SMHM ecology, such as habitat use, have been addressed extensively, others, such as the effects of environmental contamination, are largely unaddressed. We suggest that conservation and restoration-planning processes consider experimental approaches within restoration designs to address these deficiencies. Continued investment in basic and applied SMHM ecology to collect baseline and long-term data will also be beneficial. Additionally, further coordination among managers and researchers can facilitate more effective responses to uncertainties and emerging threats, especially climate change, which threatens the SMHM and its habitat throughout its range.

Most native red foxes (Vulpes vulpes) in the western contiguous United States appear to be climatically restricted to colder regions in the major mountain ranges and, in some areas, have suffered precipitous declines in abundance that may be linked to warming trends. However, another population of unknown origin has occurred in arid habitats in the Sacramento Valley of California well outside this narrow bioclimatic niche since at least 1880. If native, this population would be ecologically distinct among indigenous North American red foxes. We used mitochondrial and microsatellite markers from historical and modern samples (modes: 1910–1930 and 2000–2008, respectively) obtained throughout the western United States to determine the origins of the Sacramento Valley red fox, and assess the historical and modern connectivity and genetic effective population sizes of Sacramento Valley and montane red foxes. We found clear and consistent evidence supporting the indigenous origin of the Sacramento Valley population, including the phylogenetic positioning of the dominant, endemic mtDNA clade and microsatellite clustering of the Sacramento Valley population with the nearest montane population. Based on both mitochondrial and microsatellite AMOVAs, connectivity among Western populations of red foxes declined substantially between historical and modern time periods. Estimates based on temporal losses in gene diversity for both marker types suggest that both the Sierra Nevada (including the Southern Cascades population) and the Sacramento Valley populations have small genetic effective population sizes. Significant heterozygote excesses also indicate the occurrence of recent bottlenecks in these populations. Both substitutions distinguishing the 2 endemic Sacramento Valley haplotypes from the dominant montane haplotype were in the coding region and nonsynonymous, consistent with adaptive differences. These findings along with previously reported body size distinctions between Sacramento Valley and montane red foxes argue for distinct subspecific status for the Sacramento Valley red fox, for which we propose the designation V. v. patwin n. subsp. The small genetic effective population size estimates for the Sierra Nevada red fox and Sacramento Valley red fox are cause for concern, as is the possibility of genetic introgression into the latter population from an adjacent, recently established nonnative population.

SNPs are fast becoming the marker of choice in population genetics studies of model organisms. However, a lack of efficient means to assay sufficient numbers of SNPs in non-model organisms has prevented their widespread use for conservation-related applications. We established a SNP genotyping assay (including development of new SNP markers) for detection of genetic variation in coding and non-coding parts of the fox genome, using a 96-locus multiplex format. Coding SNPs were associated with Agouti and Mc1r coat-color alleles, phylogenetically basal mitochondrial mutations, sex markers, B-chromosome proto-oncogenes, and serotonin-receptor genes. Non-coding SNPs (n = 51) included 27 newly described microsatellite-linked SNPs. A panel of red foxes (n = 96) was used to characterize minor allele frequencies and Hardy–Weinberg equilibrium. Genotyping accuracy was 99% for 72 SNPs relative to sequenced and known-phenotype animals.

Live capture-recapture is often considered the gold standard for estimating wildlife population size or density, but the approach can be limited by permitting requirements, required labor, welfare concerns, and biased estimates resulting from heterogeneity in individual behavior. Noninvasive genetic sampling (e.g., from fecal pellets) offers a powerful alternative approach, but this method's success varies among taxa, with little research available on its use in rodents. Here, we addressed a series of questions to develop a noninvasive genetic sampling approach for the endangered giant kangaroo rat (Dipodomys ingens): (1) how quickly does DNA degrade in natural conditions, (2) how many pellets are required to recover a genotype, (3) how often do multiple individuals contaminate a pooled sample from a single sampling location, and (4) how do variable and parameter estimates from noninvasive genetic sampling compare to live-trapping mark-recapture estimates? We found that fecal pellets were successfully genotyped up to 9 days (estimated probability of recovery = 0.78) after exposure to hot, arid conditions, but that rate fell precipitously soon after. Although giant kangaroo rats are territorial, multiple individuals deposited fecal pellets at the same sampling locations; however, single pellets contained sufficient DNA to recover genotypes and to identify individuals, so contamination was not a problem for this approach. Capture probabilities were lower using noninvasive genetic sampling (= 0.26, SE = 0.01) than live trapping (= 0.40, SE = 0.06). Population estimates were generally similar using noninvasive genetic sampling, although they were quite a bit higher (= 64, = 38) on one grid. Noninvasive genetic sampling can overcome many of the limitations of live-trapping for small mammals, but the approach should be tested in additional taxa and systems to provide more generalizable recommendations for sampling schemes. [ABSTRACT FROM AUTHOR]

The Sacramento Valley red fox Vulpes vulpes patwin of California is a newly named subspecies recently found to be distinct both from other native red foxes and nearby introduced populations. The Sacramento Valley red fox experienced a historical demographic bottleneck resulting in a critically small genetic effective population size, causing concern over its current status and management requirements, yet little is known about its contemporary abundance, demographic trajectory, or habitat use. The hot, arid Sacramento Valley contrasts starkly in climate and physiography with the boreal habitats of other indigenous red foxes in western North America, indicating the need to obtain information specifically on the habitat requirements of this subspecies. A 3-y effort to locate reproductive den sites throughout the Sacramento Valley resulted in 42 independent dens, which we used to obtain preliminary information on habitat use and to develop a distribution model for this subspecies, and 28 Sacramento Valley red foxes killed by vehicles, which we used as independent data to test the models. Foxes were present significantly more than expected in grasslands and less than expected in wetlands and flooded agriculture and also tended to occur in proximity to human development, potentially as refuges from coyotes Canis latrans. We used Maxent to build predictive models. The best model, which incorporated vegetation/land-use classes and proximity to human development, identified 24% of the study area as predicted-presence habitat, which contained 76% of the den sites used to construct the model and 89% of independent locations used to test the model. Our model greatly narrowed the area over which foxes are predicted to occur and will facilitate future surveys to assess occupancy and ultimately abundance and population trends. [ABSTRACT FROM AUTHOR]